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| Status |
Public on Feb 06, 2020 |
| Title |
GF_DSS_6 [RNA-seq] |
| Sample type |
SRA |
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| Source name |
colon epithel
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| Organism |
Mus musculus |
| Characteristics |
treatment: Germ-free, DSS-treatment
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| Extracted molecule |
total RNA |
| Extraction protocol |
For epithelial cell preparation from colon, colon was flushed with ice-cold PBS, cut open longitudinally. Distal and proximal colon region were processed separately. Each part was minced into small pieces in cold PBS. Enterocytes were mechanically isolated by shaking in PBS with 30 mM EDTA, at 37oC. Crypts were recovered and then stored at -80°C for RNA extraction. Only samples from distal colon were used in our study. Total RNA from the samples was isolated using the Fibrous Tissue Kit (Qiagen) according to the manufacturer’s instructions. The Poly(A)Purist™ MAG Kit (Ambion) was used for mRNA selection.
Sequencing libraries were prepared using 1µg of DNAse-treated total RNA in the first step of the TruSeq RNA Sample Preparation v2 protocol (Illumina, Part# 15026495 Rev. A) as recommended by the manufacturer.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
counts.all
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| Data processing |
Illumina Casava1.8.1 software used for basecalling.
Preprocessing, read trimming and quality filtering: Trimmomatic 0.39
Transcriptome mapping: Tophat 2.0.6
computation of count data: htseq.py
Genome_build: mm9
Supplementary_files_format_and_content: count table containing the count values for all genes in all samples
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| Submission date |
Sep 04, 2019 |
| Last update date |
Feb 06, 2020 |
| Contact name |
Guenter Raddatz |
| Organization name |
German Center for Cancer Research
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| Street address |
Im Neuenheimer Feld 580
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| City |
Heidelberg |
| ZIP/Postal code |
69120 |
| Country |
Germany |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE136840 |
The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation [RNA-seq] |
| GSE137037 |
The intestinal microbiota programs DNA methylation to control tissue homeostasis and inflammation |
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| Relations |
| BioSample |
SAMN12690762 |
| SRA |
SRX6799959 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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